DEMO TO CREATE ANIMATED GIFS FROM NEURON

                          Alain Destexhe

            Department of Physiology, Laval University,
                      Quebec G1K 7P4, Canada

Present address: CNRS, UNIC (Bat-33), Avenue de la Terrasse,
                 91198 Gif-sur-Yvette, France

                      Destexhe@iaf.cnrs-gif.fr
                     http://cns.iaf.cnrs-gif.fr


This package is running with the NEURON simulation program written by Michael
Hines and available on internet at: http://www.neuro.duke.edu/neuron/home.html

The package illustrates how to create animated gif movies from NEURON.  The
example taken generates an animation of the somato-dendritic profile of
membrane potential in a model of thalamic reticular neuron, relative to the
paper:

  Destexhe A, Contreras D, Steriade M, Sejnowski TJ and Huguenard JR.  
  In vivo, in vitro and computational analysis of dendritic calcium currents 
  in thalamic reticular neurons.  Journal of Neuroscience 16: 169-185, 1996.
  (see http://cns.iaf.cnrs-gif.fr in "publications")




  SYSTEM REQUIREMENTS
  ===================

Animated gifs can be played using the browser Netscape.  To generate animated
gifs from NEURON, additional packages must be installed besides those already
present in NEURON: 

1. ghostscript

Ghostscript is a public-domain postscript interpreter available at many sites
deserving gnu licenses.  See for example:
  http://www.cs.wisc.edu/~ghost
  ftp://prep.ai.mit.edu/pub/gnu/

2. pstopnm and ppmtogif

The scripts pstopnm and ppmtogif are part of the PBMplus and Netpbm packages
(freely available).  pstopnm uses ghostscript to transform postscript files
into ppm format.  The transformation to gif is then made using ppmtogif.  For
more details see: 
  http://www-bioeng.ucsd.edu/~fvetter/misc/postscript-faq.txt
  http://www.cs.ucsb.edu/Facilities/Software/netpbm.html
  http://toons.cs.ucsb.edu:4080/man?pstopnm 
  http://toons.cs.ucsb.edu:4080/man?ppmtogif
The Netpbm package can be obtained at:
  ftp://ftp.cs.ubc.ca/ftp/archive/netpbm/
A copy of the pstopnm script can also be downloaded at:
  http://cns.iaf.cnrs-gif.fr/files/pstopnm

2. whirlgif

Whirlgif is a publically-available program that combines gif frames into an
animated gif file.  The source code of this program is available at:
  http://www.msg.net/utility/whirlgif
  http://eigen.ee.ualberta.ca/ftp/hpux/Networking/WWW/whirlgif-2.01/whirlgif-2.01-ss-10.20.tar.gz




  PROCEDURE
  =========

Creating an animated gif movie from NEURON simulations can be done in the
following steps: (a) save NEURON plots as postscript; (b) convert postscript
images into gif; (c) encode the gif files into an animated gif.

Steps (a) and (b) can be done in NEURON if the commands "pstopnm" and
"ppmtogif" are available.  This is what shows the demo called "re80gif.oc". 
The demo creates a series of successive gif frames from a NEURON simulation
and name them: 
	0000.gif, 0001.gif, 0002.gif, ...  
To run this demo, do the following: 
	- enter the command "special re80gif.oc -"
	- set "Shape Style" to "Show Diam" in the shapeplot
	  (the "v" can be moved outside the plot using "move text" if needed)
	- set the shapeplot in "Shape Plot" mode
	- click on "run"
The program will create a bunch of frames in a directory called "frames". 

Generating the animated gif movie from the frames (step c) can be done using
the "whirlgif" program; enter the command:
	whirlgif frames/* > dendritRE.gif
The program will create an animated gif file called "dendritRE.gif" of the
NEURON simulation.  This movie file can be viewed at:
   http://cns.iaf.cnrs-gif.fr/files/dendritRE.gif
(see documentation of whirlgif for details on how to change the parameters
of the movie)

At the end, destroy the gif frames which are not needed anymore



  MOVIES USING THE WINDOW MANAGER
  ===============================

More sophisticate animations can be done using the print-window-manager (PWM).
In this case, uncomment the appropriate commands in the oc file (replace the
"g[sh].printfile..." by "print_session..." command).  Then start the program
and select/arrange windows as desired on the paper icon of the PWM.  Then run
the program as above, the difference is that each frame will contain the
complete set of windows as arranged by the user.  (this allows for instance to
generate movies where both shape plot and time plots appear - see examples in
http://cns.iaf.cnrs-gif.fr)




  CONDITIONS AND TROUBLESHOOTING
  ==============================

This demo is provided "as is" and is of free access - if you experience
problems installing ghostscript, pstopnm, ppmtogif or whirlgif, please refer
directly to the authors of these programs.  If these commands are properly
installed, the demo should work straight.  If you notice platform-specific
problems, please send me a note, so that I can maintain a list of installation
instructions if needed.


Alain Destexhe

CNRS, UNIC (Bat-33), 
Avenue de la Terrasse,
91198 Gif-sur-Yvette, France

email: Destexhe@iaf.cnrs-gif.fr
http://cns.iaf.cnrs-gif.fr

Thanks to John Huguenard (Stanford University) who created a preliminary
version of this program.